R Under development (unstable) (2024-07-08 r86886 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(biosys)
> 
> test_check("biosys")
Running command d:\rtools44\usr\bin\perl.exe --help

Usage: /usr/bin/perl [switches] [--] [programfile] [arguments]
  -0[octal/hexadecimal] specify record separator (\0, if no argument)
  -a                    autosplit mode with -n or -p (splits $_ into @F)
  -C[number/list]       enables the listed Unicode features
  -c                    check syntax only (runs BEGIN and CHECK blocks)
  -d[t][:MOD]           run program under debugger or module Devel::MOD
  -D[number/letters]    set debugging flags (argument is a bit mask or alphabets)
  -e commandline        one line of program (several -e's allowed, omit programfile)
  -E commandline        like -e, but enables all optional features
  -f                    don't do $sitelib/sitecustomize.pl at startup
  -F/pattern/           split() pattern for -a switch (//'s are optional)
  -g                    read all input in one go (slurp), rather than line-by-line (alias for -0777)
  -i[extension]         edit <> files in place (makes backup if extension supplied)
  -Idirectory           specify @INC/#include directory (several -I's allowed)
  -l[octnum]            enable line ending processing, specifies line terminator
  -[mM][-]module        execute "use/no module..." before executing program
  -n                    assume "while (<>) { ... }" loop around program
  -p                    assume loop like -n but print line also, like sed
  -s                    enable rudimentary parsing for switches after programfile
  -S                    look for programfile using PATH environment variable
  -t                    enable tainting warnings
  -T                    enable tainting checks
  -u                    dump core after parsing program
  -U                    allow unsafe operations
  -v                    print version, patchlevel and license
  -V[:configvar]        print configuration summary (or a single Config.pm variable)
  -w                    enable many useful warnings
  -W                    enable all warnings
  -x[directory]         ignore text before #!perl line (optionally cd to directory)
  -X                    disable all warnings
  
Run 'perldoc perl' for more help with Perl.

Running command d:\rtools44\usr\bin\gzip.exe -c D:\temp\Rtmpw7AZE4\file23c901a795e1a | d:\rtools44\usr\bin\gzip.exe -d > D:\temp\Rtmpw7AZE4\file23c906aa72d3

gzip: D:\temp\Rtmpw7AZE4\file23c901a795e1a: not in gzip format
gzip: |.gz: No such file or directory

gzip: d:\rtools44\usr\bin\gzip.exe: not in gzip format
gzip: >.gz: No such file or directory
gzip: D:\temp\Rtmpw7AZE4\file23c906aa72d3.gz: No such file or directory
[ FAIL 1 | WARN 2 | SKIP 11 | PASS 9 ]

══ Skipped tests (11) ══════════════════════════════════════════════════════════
• .Platform$OS.type == "windows" is TRUE (1): 'test-utils.R:20:5'
• empty test (1): 'test-exec.R:35:1'
• nzchar(Sys.which("alleleCounter")) is not TRUE (1): 'test-exec.R:2:5'
• nzchar(Sys.which("cellranger")) is not TRUE (1): 'test-exec.R:7:5'
• nzchar(Sys.which("fastq_pair")) is not TRUE (1): 'test-exec.R:12:5'
• nzchar(Sys.which("gistic2")) is not TRUE (1): 'test-exec.R:17:5'
• nzchar(Sys.which("kraken2")) is not TRUE (1): 'test-exec.R:31:5'
• nzchar(Sys.which("python2")) || nzchar(Sys.which("python3")) is not TRUE (2):
  'test-exec.R:22:5', 'test-exec.R:41:5'
• nzchar(Sys.which("run-trust4")) is not TRUE (1): 'test-exec.R:53:5'
• nzchar(Sys.which("seqkit")) is not TRUE (1): 'test-exec.R:48:5'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-exec.R:67:5'): `pipe()` method works well ──────────────────────
Error in `file(con, "rb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─testthat::expect_identical(read_lines(file), read_lines(file2)) at test-exec.R:67:5
 2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─biosys:::read_lines(file2)
 5.   └─biosys:::is_gzip_signature(file)
 6.     └─biosys:::match_file_signature(...)
 7.       ├─file_signature %||% readBin(file, raw(), n)
 8.       └─base::readBin(file, raw(), n)
 9.         └─base::file(con, "rb")

[ FAIL 1 | WARN 2 | SKIP 11 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
   1.43    0.29    1.92